Variant report

Variant	rs12317467
Chromosome Location	chr12:104577494-104577495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104577047..104579321-chr12:104581007..104583445,2	MCF-7	breast:
2	chr12:104571005..104572580-chr12:104577210..104579491,2	MCF-7	breast:
3	chr12:104530299..104532759-chr12:104575223..104579205,3	MCF-7	breast:
4	chr12:104575420..104578369-chr12:104681215..104683180,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11111896	0.88[YRI][hapmap]
rs11111920	0.82[ASN][1000 genomes]
rs11111933	0.88[YRI][hapmap]
rs11610133	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610541	0.97[ASN][1000 genomes]
rs11610612	0.87[ASN][1000 genomes]
rs11615168	0.80[ASN][1000 genomes]
rs12300246	0.80[ASN][1000 genomes]
rs12304631	0.82[ASN][1000 genomes]
rs12305190	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs12307391	0.80[ASN][1000 genomes]
rs12310380	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs12313776	0.80[ASN][1000 genomes]
rs12318352	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs17035279	0.81[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17035291	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765111	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4255604	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4338595	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4964251	0.89[ASN][1000 genomes]
rs59014318	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73394538	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104576600-104577600	Enhancers	Hela-S3	cervix
2	chr12:104576600-104578200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:104576800-104577600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
4	chr12:104576800-104578600	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:104577000-104577800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:104577000-104578200	ZNF genes & repeats	Osteobl	bone
7	chr12:104577000-104578400	ZNF genes & repeats	A549	lung
8	chr12:104577000-104578600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:104577000-104578600	ZNF genes & repeats	Placenta	Placenta
10	chr12:104577200-104577800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:104577200-104578200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr12:104577200-104578800	ZNF genes & repeats	Liver	Liver
13	chr12:104577400-104577600	Weak transcription	Pancreas	Pancrea

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